1
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Zhao Z, He S, Yu X, Lai X, Tang S, Mariya M. EA, Wang M, Yan H, Huang X, Zeng S, Zha D. Analysis and Experimental Validation of Rheumatoid Arthritis Innate Immunity Gene CYFIP2 and Pan-Cancer. Front Immunol 2022; 13:954848. [PMID: 35898498 PMCID: PMC9311328 DOI: 10.3389/fimmu.2022.954848] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/13/2022] [Indexed: 01/22/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, heterogeneous autoimmune disease. Its high disability rate has a serious impact on society and individuals, but there is still a lack of effective and reliable diagnostic markers and therapeutic targets for RA. In this study, we integrated RA patient information from three GEO databases for differential gene expression analysis. Additionally, we also obtained pan-cancer-related genes from the TCGA and GTEx databases. For RA-related differential genes, we performed functional enrichment analysis and constructed a weighted gene co-expression network (WGCNA). Then, we obtained 490 key genes by intersecting the significant module genes selected by WGCNA and the differential genes. After using the RanddomForest, SVM-REF, and LASSO three algorithms to analyze these key genes and take the intersection, based on the four core genes (BTN3A2, CYFIP2, ST8SIA1, and TYMS) that we found, we constructed an RA diagnosis. The nomogram model showed good reliability and validity after evaluation, and the ROC curves of the four genes showed that these four genes played an important role in the pathogenesis of RA. After further gene correlation analysis, immune infiltration analysis, and mouse gene expression validation, we finally selected CYFIP2 as the cut-in gene for pan-cancer analysis. The results of the pan-cancer analysis showed that CYFIP2 was closely related to the prognosis of patients with various tumors, the degree of immune cell infiltration, as well as TMB, MSI, and other indicators, suggesting that this gene may be a potential intervention target for human diseases including RA and tumors.
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Affiliation(s)
- ZhenYu Zhao
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - ShaoJie He
- Department of Orthopaedics, Panyu Hospital of Chinese Medicine, Guangzhou, China
| | - XinCheng Yu
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - XiaoFeng Lai
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Sheng Tang
- Department of Orthopedics, The Sixth Affiliated Hospital, South China University of Technology, Foshan, China
| | - El Akkawi Mariya M.
- Department of Plastic and Reconstructive Surgery, ZhuJiang Hospital of Southern Medical University, GuangZhou, China
| | - MoHan Wang
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Hai Yan
- Department of Medicine, Flushing Hospital Medical Center, Flushing, NY, United States
| | - XingQi Huang
- Department of Neurosurgery , General Hospital of Tianjin Medical University, China
| | - Shan Zeng
- Department of Rheumatology, The First Affiliated Hospital, Jinan University, Guangzhou, China
- *Correspondence: Dingsheng Zha, ; Shan Zeng,
| | - DingSheng Zha
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
- *Correspondence: Dingsheng Zha, ; Shan Zeng,
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2
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Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya, North East India reveals novel genes. Genomics 2017; 110:112-123. [PMID: 28890207 DOI: 10.1016/j.ygeno.2017.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/22/2022]
Abstract
Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes were found to be similar to that of the TCGA-HNSCC study some of which are TSGs and few novel genes which may serve as candidate methylation biomarkers for OSCC in this poorly characterized ethnic group.
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3
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Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI. Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage. Cancer Cell 2016; 30:806-821. [PMID: 27846393 PMCID: PMC5805090 DOI: 10.1016/j.ccell.2016.09.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/18/2016] [Accepted: 09/19/2016] [Indexed: 01/17/2023]
Abstract
We analyzed the in silico purified DNA methylation signatures of 82 mantle cell lymphomas (MCL) in comparison with cell subpopulations spanning the entire B cell lineage. We identified two MCL subgroups, respectively carrying epigenetic imprints of germinal-center-inexperienced and germinal-center-experienced B cells, and we found that DNA methylation profiles during lymphomagenesis are largely influenced by the methylation dynamics in normal B cells. An integrative epigenomic approach revealed 10,504 differentially methylated regions in regulatory elements marked by H3K27ac in MCL primary cases, including a distant enhancer showing de novo looping to the MCL oncogene SOX11. Finally, we observed that the magnitude of DNA methylation changes per case is highly variable and serves as an independent prognostic factor for MCL outcome.
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Affiliation(s)
- Ana C Queirós
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Renée Beekman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Roser Vilarrasa-Blasi
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Martí Duran-Ferrer
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Angelika Merkel
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Emanuele Raineri
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Nuria Russiñol
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Giancarlo Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Alba Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Marta Kulis
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Núria Verdaguer-Dot
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Pedro Jares
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Unidad de Genómica, IDIBAPS, Barcelona 08036, Spain
| | | | | | - Anke Bergmann
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany; Department of Pediatrics, Christian-Albrechts University & University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Inga Vater
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Itziar Salaverría
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Harmen J G van de Werken
- Department of Cell Biology, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Cancer Computational Biology Center, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Department of Urology, Erasmus MC, Rotterdam 3015 CN, the Netherlands
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Romina Royo
- Joint Program on Computational Biology, Barcelona Supercomputing Center (BSC) and Institute of Research in Biomedicine (IRB), Barcelona Science Park, Barcelona 08034, Spain
| | - Joost Martens
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Eva Giné
- Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona 08036, Spain
| | | | - Hendrik G Stunnenberg
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Wolfram Klapper
- Hematopathology Section and Lymph Node Registry, Christian-Albrecht University, Kiel 24105, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel 24116, Germany
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Elías Campo
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain; Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Barcelona 08036, Spain
| | - José I Martín-Subero
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain.
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4
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Mansouri L, Rosenquist R. Unraveling the DNA Methylome in Mantle Cell Lymphoma: New Insights into the Cellular Origin. Cancer Cell 2016; 30:665-667. [PMID: 27846388 DOI: 10.1016/j.ccell.2016.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Our understanding of the DNA methylome and its impact on cancer evolution and disease progression is rapidly evolving. In this issue of Cancer Cell, Queirós et al. provide a detailed characterization of the DNA methylome in mantle cell lymphoma and reveal novel molecular subtypes, potentially with different cellular origins.
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Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden.
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5
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Subhash S, Andersson PO, Kosalai ST, Kanduri C, Kanduri M. Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL. Clin Epigenetics 2016; 8:106. [PMID: 27777635 PMCID: PMC5062931 DOI: 10.1186/s13148-016-0274-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022] Open
Abstract
Background Methyl-CpG-binding domain protein enriched genome-wide sequencing (MBD-Seq) is a robust and powerful method for analyzing methylated CpG-rich regions with complete genome-wide coverage. In chronic lymphocytic leukemia (CLL), the role of CpG methylated regions associated with transcribed long noncoding RNAs (lncRNA) and repetitive genomic elements are poorly understood. Based on MBD-Seq, we characterized the global methylation profile of high CpG-rich regions in different CLL prognostic subgroups based on IGHV mutational status. Results Our study identified 5800 hypermethylated and 12,570 hypomethylated CLL-specific differentially methylated genes (cllDMGs) compared to normal controls. From cllDMGs, 40 % of hypermethylated and 60 % of hypomethylated genes were mapped to noncoding RNAs. In addition, we found that the major repetitive elements such as short interspersed elements (SINE) and long interspersed elements (LINE) have a high percentage of cllDMRs (differentially methylated regions) in IGHV subgroups compared to normal controls. Finally, two novel lncRNAs (hypermethylated CRNDE and hypomethylated AC012065.7) were validated in an independent CLL sample cohort (48 samples) compared with 6 normal sorted B cell samples using quantitative pyrosequencing analysis. The methylation levels showed an inverse correlation to gene expression levels analyzed by real-time quantitative PCR. Notably, survival analysis revealed that hypermethylation of CRNDE and hypomethylation of AC012065.7 correlated with an inferior outcome. Conclusions Thus, our comprehensive methylation analysis by MBD-Seq provided novel hyper and hypomethylated long noncoding RNAs, repetitive elements, along with protein coding genes as potential epigenetic-based CLL-signature genes involved in disease pathogenesis and prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0274-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden ; Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, S-413 45 Gothenburg, Sweden
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6
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Kopparapu PK, Bhoi S, Mansouri L, Arabanian LS, Plevova K, Pospisilova S, Wasik AM, Croci GA, Sander B, Paulli M, Rosenquist R, Kanduri M. Epigenetic silencing of miR-26A1 in chronic lymphocytic leukemia and mantle cell lymphoma: Impact on EZH2 expression. Epigenetics 2016; 11:335-43. [PMID: 27052808 DOI: 10.1080/15592294.2016.1164375] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Downregulation of miR26A1 has been reported in various B-cell malignancies; however, the mechanism behind its deregulation remains largely unknown. We investigated miR26A1 methylation and expression levels in a well-characterized series of chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL). From 450K methylation arrays, we first observed miR26A1 (cg26054057) as uniformly hypermethylated in MCL (n = 24) (all >75%), while CLL (n = 18) showed differential methylation between prognostic subgroups. Extended analysis using pyrosequencing confirmed our findings and real-time quantitative PCR verified low miR26A1 expression in both CLL (n = 70) and MCL (n = 38) compared to normal B-cells. Notably, the level of miR26A1 methylation predicted outcome in CLL, with higher levels seen in poor-prognostic, IGHV-unmutated CLL. Since EZH2 was recently reported as a target for miR26A1, we analyzed the expression levels of both miR26A1 and EZH2 in primary CLL samples and observed an inverse correlation. By overexpression of miR26A1 in CLL and MCL cell lines, reduced EZH2 protein levels were observed using both Western blot and flow cytometry. In contrast, methyl-inhibitor treatment led to upregulated miR26A1 expression with a parallel decrease of EZH2 expression. Finally, increased levels of apoptosis were observed in miR26A1-overexpressing cell lines, further underscoring the functional relevance of miR26A1. In summary, we propose that epigenetic silencing of miR26A1 is required for the maintenance of increased levels of EZH2, which in turn translate into a worse outcome, as shown in CLL, highlighting miR26A1 as a tumor suppressor miRNA.
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Affiliation(s)
- Pradeep Kumar Kopparapu
- a Department of Clinical Chemistry and Transfusion Medicine , Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University , Sweden
| | - Sujata Bhoi
- b Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala , Sweden
| | - Larry Mansouri
- b Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala , Sweden
| | - Laleh S Arabanian
- a Department of Clinical Chemistry and Transfusion Medicine , Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University , Sweden
| | - Karla Plevova
- c Central European Institute of Technology, Masaryk University and University Hospital Brno , Czech Republic
| | - Sarka Pospisilova
- c Central European Institute of Technology, Masaryk University and University Hospital Brno , Czech Republic
| | - Agata M Wasik
- d Department of Laboratory Medicine , Division of Pathology, Karolinska University Hospital , Sweden
| | | | - Birgitta Sander
- d Department of Laboratory Medicine , Division of Pathology, Karolinska University Hospital , Sweden
| | - Marco Paulli
- e Department of Molecular Medicine , University of Pavia , Italy
| | - Richard Rosenquist
- b Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala , Sweden
| | - Meena Kanduri
- a Department of Clinical Chemistry and Transfusion Medicine , Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University , Sweden
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7
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Wong Doo N, Makalic E, Joo JE, Vajdic CM, Schmidt DF, Wong EM, Jung CH, Severi G, Park DJ, Chung J, Baglietto L, Prince HM, Seymour JF, Tam C, Hopper JL, English DR, Milne RL, Harrison SJ, Southey MC, Giles GG. Global measures of peripheral blood-derived DNA methylation as a risk factor in the development of mature B-cell neoplasms. Epigenomics 2015; 8:55-66. [PMID: 26679037 DOI: 10.2217/epi.15.97] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AIM To examine whether peripheral blood methylation is associated with risk of developing mature B-cell neoplasms (MBCNs). MATERIALS & METHODS We conducted a case-control study nested within a large prospective cohort. Peripheral blood was collected from healthy participants. Cases of MBCN were identified by linkage to cancer registries. Methylation was measured using the Infinium(®) HumanMethylation450. RESULTS During a median of 10.6-year follow-up, 438 MBCN cases were evaluated. Global hypomethylation was associated with increased risk of MBCN (odds ratio: 2.27, [95% CI: 1.59-3.25]). Within high CpG promoter regions, hypermethylation was associated with increased risk (odds ratio: 1.76 [95% CI: 1.25-2.48]). Promoter hypermethylation was observed in HOXA9 and CDH1 genes. CONCLUSION Aberrant global DNA methylation is detectable in peripheral blood collected years before diagnosis and is associated with increased risk of MBCN, suggesting changes to DNA methylation are an early event in MBCN development.
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Affiliation(s)
- Nicole Wong Doo
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Concord General & Repatriation Hospital, NSW, Australia
| | - Enes Makalic
- Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - JiHoon E Joo
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Claire M Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Ee Ming Wong
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Chol-Hee Jung
- VLSCI Life Sciences Computation Centre, The University of Melbourne, Victoria, Australia
| | | | - Daniel J Park
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Jessica Chung
- VLSCI Life Sciences Computation Centre, The University of Melbourne, Victoria, Australia
| | - Laura Baglietto
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Henry Miles Prince
- Department of Haematology, Peter MacCallum Cancer Centre, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - John F Seymour
- Department of Haematology, Peter MacCallum Cancer Centre, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Constantine Tam
- Department of Haematology, Peter MacCallum Cancer Centre, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Simon J Harrison
- Department of Haematology, Peter MacCallum Cancer Centre, Victoria, Australia
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
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8
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Magni M, Nicola MD, Patti C, Scimè R, Mulè A, Rambaldi A, Intermesoli T, Viero P, Tarella C, Gueli A, Bergui L, Trentin L, Barzan A, Benedetti F, Ambrosetti A, Di Raimondo F, Chiarenza A, Parvis G, Billio A, Attolico I, Olivieri A, Montanari M, Carlo-Stella C, Matteucci P, Devizzi L, Guidetti A, Viviani S, Valagussa P, Gianni AM. Results of a randomized trial comparing high-dose chemotherapy plus Auto-SCT and R-FC in CLL at diagnosis. Bone Marrow Transplant 2014; 49:485-91. [DOI: 10.1038/bmt.2013.214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/19/2013] [Accepted: 11/19/2013] [Indexed: 11/09/2022]
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9
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Kanduri M, Sander B, Ntoufa S, Papakonstantinou N, Sutton LA, Stamatopoulos K, Kanduri C, Rosenquist R. A key role for EZH2 in epigenetic silencing of HOX genes in mantle cell lymphoma. Epigenetics 2013; 8:1280-8. [PMID: 24107828 DOI: 10.4161/epi.26546] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The chromatin modifier EZH2 is overexpressed and associated with inferior outcome in mantle cell lymphoma (MCL). Recently, we demonstrated preferential DNA methylation of HOX genes in MCL compared with chronic lymphocytic leukemia (CLL), despite these genes not being expressed in either entity. Since EZH2 has been shown to regulate HOX gene expression, to gain further insight into its possible role in differential silencing of HOX genes in MCL vs. CLL, we performed detailed epigenetic characterization using representative cell lines and primary samples. We observed significant overexpression of EZH2 in MCL vs. CLL. Chromatin immune precipitation (ChIP) assays revealed that EZH2 catalyzed repressive H3 lysine 27 trimethylation (H3K27me3), which was sufficient to silence HOX genes in CLL, whereas in MCL H3K27me3 is accompanied by DNA methylation for a more stable repression. More importantly, hypermethylation of the HOX genes in MCL resulted from EZH2 overexpression and subsequent recruitment of the DNA methylation machinery onto HOX gene promoters. The importance of EZH2 upregulation in this process was further underscored by siRNA transfection and EZH2 inhibitor experiments. Altogether, these observations implicate EZH2 in the long-term silencing of HOX genes in MCL, and allude to its potential as a therapeutic target with clinical impact.
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Affiliation(s)
- Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; Gothenburg University; Gothenburg, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine; Division of Pathology; Karolinska Institutet and Karolinska University Hospital; Huddinge, Sweden
| | - Stavroula Ntoufa
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Nikos Papakonstantinou
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala, Sweden
| | - Kostas Stamatopoulos
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Chandrasekhar Kanduri
- Department of Medical and Clinical Genetics; Department of Biomedicine; The Sahlgrenska Academy; Gothenburg University; Gothenburg, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala, Sweden
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10
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11
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Enjuanes A, Albero R, Clot G, Navarro A, Beà S, Pinyol M, Martín-Subero JI, Klapper W, Staudt LM, Jaffe ES, Rimsza L, Braziel RM, Delabie J, Cook JR, Tubbs RR, Gascoyne R, Connors JM, Weisenburger DD, Greiner TC, Chan WC, López-Guillermo A, Rosenwald A, Ott G, Campo E, Jares P. Genome-wide methylation analyses identify a subset of mantle cell lymphoma with a high number of methylated CpGs and aggressive clinicopathological features. Int J Cancer 2013; 133:2852-63. [PMID: 23754783 DOI: 10.1002/ijc.28321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 04/23/2013] [Indexed: 01/02/2023]
Abstract
Mantle cell lymphoma (MCL) is a B-cell neoplasm with an aggressive clinical behavior characterized by the t(11;14)(q13;q32) and cyclin D1 overexpression. To clarify the potential contribution of altered DNA methylation in the development and/or progression of MCL, we performed genome-wide methylation profiling of a large cohort of primary MCL tumors (n = 132), MCL cell lines (n = 6) and normal lymphoid tissue samples (n = 31), using the Infinium HumanMethylation27 BeadChip. DNA methylation was compared to gene expression, chromosomal alterations and clinicopathological parameters. Primary MCL displayed a heterogeneous methylation pattern dominated by DNA hypomethylation when compared to normal lymphoid samples. A total of 454 hypermethylated and 875 hypomethylated genes were identified as differentially methylated in at least 10% of primary MCL. Annotation analysis of hypermethylated genes recognized WNT pathway inhibitors and several tumor suppressor genes as frequently methylated, and a substantial fraction of these genes (22%) showed a significant downregulation of their transcriptional levels. Furthermore, we identified a subset of tumors with extensive CpG methylation that had an increased proliferation signature, higher number of chromosomal alterations and poor prognosis. Our results suggest that a subset of MCL displays a dysregulation of DNA methylation characterized by the accumulation of CpG hypermethylation highly associated with increased proliferation that may influence the clinical behavior of the tumors.
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Affiliation(s)
- Anna Enjuanes
- Genomics Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
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Vecchio L, Seke Etet PF, Kipanyula MJ, Krampera M, Nwabo Kamdje AH. Importance of epigenetic changes in cancer etiology, pathogenesis, clinical profiling, and treatment: what can be learned from hematologic malignancies? Biochim Biophys Acta Rev Cancer 2013; 1836:90-104. [PMID: 23603458 DOI: 10.1016/j.bbcan.2013.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/25/2013] [Accepted: 04/10/2013] [Indexed: 02/06/2023]
Abstract
Epigenetic alterations represent a key cancer hallmark, even in hematologic malignancies (HMs) or blood cancers, whose clinical features display a high inter-individual variability. Evidence accumulated in recent years indicates that inactivating DNA hypermethylation preferentially targets the subset of polycomb group (PcG) genes that are regulators of developmental processes. Conversely, activating DNA hypomethylation targets oncogenic signaling pathway genes, but outcomes of both events lead in the overexpression of oncogenic signaling pathways that contribute to the stem-like state of cancer cells. On the basis of recent evidence from population-based, clinical and experimental studies, we hypothesize that factors associated with risk for developing a HM, such as metabolic syndrome and chronic inflammation, trigger epigenetic mechanisms to increase the transcriptional expression of oncogenes and activate oncogenic signaling pathways. Among others, signaling pathways associated with such risk factors include pro-inflammatory nuclear factor κB (NF-κB), and mitogenic, growth, and survival Janus kinase (JAK) intracellular non-receptor tyrosine kinase-triggered pathways, which include signaling pathways such as transducer and activator of transcription (STAT), Ras GTPases/mitogen-activated protein kinases (MAPKs)/extracellular signal-related kinases (ERKs), phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR), and β-catenin pathways. Recent findings on epigenetic mechanisms at work in HMs and their importance in the etiology and pathogenesis of these diseases are herein summarized and discussed. Furthermore, the role of epigenetic processes in the determination of biological identity, the consequences for interindividual variability in disease clinical profile, and the potential of epigenetic drugs in HMs are also considered.
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Affiliation(s)
- Lorella Vecchio
- Laboratory of Cytometry, Institute of Molecular Genetics, CNR, University of Pavia, 27100 Pavia, Italy
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